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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="beautify_fasta" name="Beautify_FASTA" version="1.0">
2 <description>Converts interleaved FASTA to non-interleaved</description>
3 <command interpreter="perl">
4 beautify_fasta.pl $infile $outfile $delpipes $convgi $delslash $renumber $space
5 </command>
6 <inputs>
7 <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
8 <param name='delpipes' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert Pipes' help='Convert pipe symbols in fasta sequence id to space.'/>
9 <param name='convgi' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert gi|' help='Converts instances of gi| to gi_.'/>
10 <param name='delslash' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert slash \ ' help='Converts instances of \ to _.'/>
11 <param name='renumber' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Add a unique number' help='Sequentially add a unique number to beginning of each sequence.'/>
12 <param name='space' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Add a unique number' help='Add a space after the unique number.'/>
13 </inputs>
14 <outputs>
15 <data format="fasta" name="outfile" label="${tool.name} on ${on_string}: Out file" />
16 </outputs>
17 <help>**What it does**
18
19 Input an interleaved FASTA file. Beautify_FASTA converts interleaved FASTA to
20 non-interleaved (full sequence on one line). In addition, you can choose to
21 convert symbols from the FASTA ID. The FASTA ID is the descriptor from the >
22 to the first space. The FASTA description (first line after any space) is not changed.
23
24 ------
25
26 **Inputs**
27
28 Interleaved FASTA file.
29
30 ------
31
32 **Outputs**
33
34 Non-interleaved FASTA file with optional modifications to the FASTA ID.
35
36 -------
37
38 **Additional Information**
39
40 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
41 osiris_phylogenetics site at bitbucket.org
42
43 ------
44
45 **Citations**
46
47 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please
48 consider citing the following.
49
50 Current Osiris Citation is here
51
52 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
53
54 </help>
55 </tool>